Reload of ARSENAL
by The Sage of Toads
Summary: ARSENAL, reworked, improved, and with numerous things added and removed. Shinji Ikari arrives at Nerv with a mission to save humanity from the Angels, Seele, Nerv, and itself. Strap in and put on your flak vests, because it's gonna be a bloodbath.
1. Click Click, Boom

The Sage of Toads: This is a Disclaimer, brought to you in part by Shinji Ikari. (Shinji: Tell them the views…) The views and events written here are totally fucked, (Shinji: Tell them…) and not necessarily the views of anyone. (Shinji: Tell them not to take it…) However, the events and suggestions that appear in this story are not to be taken lightly. (Shinji: Tell them not to…) Children should not be reading this story, with firearms in the house. (Shinji: Tell them…) The Sage of Toads and Andrew Joshua Talon are NOT responsible for your actions. (Shinji: Tell them they agreed…) Upon reading past this disclaimer, you have agreed NOT to try this at home.

Shinji: Yeah.

The Sage of Toads: A-anything else?

Shinji: Yeah, guns don't kill people, people kill people.

**Reload of ARSENAL**  
Click-Click, Boom

"_After all of that, that's all you can say? 'I'm sorry'?"_

"…"

"_No, you can go to Hell, Father."_

**[1.]**

From the moment he got the long and thoughtful letter from his Father that politely requested his presence, Shinji Ikari had been experiencing an odd sense of déjà vu that he had been expecting as much as hoping was nothing more than another symptom of mental illness. So far, he was disappointed to find he wasn't going insane, as he stood in front of a payphone, repeatedly trying to raise his Father on the line. A large metal briefcase in hand attached to his wrist with a shackle would've drawn stares to him were he not the only person in the empty street on the outskirts of Tokyo-3.

"Come on pick up, I'm on my last coin," he pleaded into the receiver.

"We're sorry, all lines are currently down," replied a spitefully monotone automated voice.

Not that he heard it. "Just connect me to Gendo Ikari's cell phone, please!"

"We're sorry, all lines are currently down," it replied, and he imagined zeroes and ones pulling into a wicked snarl.

Smashing the phone with his case suddenly felt like a great idea, and he was halfway through that very act and screaming "WELL FUCK YOUR LINES!" at the top of his lungs before he realized it and stopped himself. On the bright side, he got his money back and a sliver of catharsis. He was on his hands and knees, happily scooping up yen coins and bills into his backpack when the explosion interrupted him.

As the obnoxious roar of humankind's feeble attempt at destroying the Third Angel flooded his ears, he remained crouched on the floor, unable to bring himself to look up. His expression was stoic, serenity that from afar would be perceived as poetic, almost beautiful in observance. He was, as Rage of the Machine tended to scream, calm like a bomb.

He stood, turned, and looked up at the Third Angel, its mask-like face regarding the weapons of man with curiosity as they failed against its indomitable might. He felt no fear, even as heat and force washed over him, only anger, growing, burning anger that was going to become an ulcer tomorrow. His health wasn't a pressing concern, making sure others were concerned for their own was a much higher priority.

"I'm going to kill him to death," he said before Misato pulled up in her Alpine, shouting for him to get in as the Angel began to thrash around.

Calmly he complied and walked over to the car, slipping inside and even buckling himself in without worry as Misato rounded the corner to avoid her car becoming a low-rider in the worst way.

"Sorry I'm late." Misato glanced at Shinji, her ebbing adrenaline rush giving her a moment to note the aloof air coming off him. Odd, he didn't seem at all bothered that he had almost been killed by, or that they were driving away from, a horrible alien monster.

"Are you okay?" She asked.

"I'm alright, please keep driving," Shinji replied, as he tightened his grip on the heavy case.

Odd was becoming weird as she glanced down at the case briefly. "So, what's that?"

"It's a suitcase nuclear bomb, six kiloton yield," Shinji replied.

Misato nearly swerved the car as she looked at him, but somehow managed to stay on the mountain road. She looked down at his suitcase, and then let out a small laugh. "Hah, you have an interesting sense of humor."

She returned her attention to the road. Shinji looked at her and began to stare. The picture really didn't do justice, but it was a good first impression, in person Misato appeared a lovely woman, but he had only these few heart-pounding moments to go with. What sort of person was she really? Well, judging by those melons that she sported and had no problem displaying, she was one of those lewd women types. He didn't know what to think of that, other than the usual thoughts a teenager would have.

"My tits are great, aren't they?"

Shinji's face went red as her jacket.

Well, there he had it. Turning to look out the passenger window to let his blush fade, he noticed that they had entered a tunnel. His eyes widened and he screamed. "STOP THE CAR, NOW!"

The Alpine's tires screamed as Misato slammed on the brakes, the car fishtailing from side to side as it went from a hundred thirty kilometers per hour to zero. Misato looked at him, startled. "What? What is it?"

Shinji's free hand had been on the dashboard to brace from the sudden stop. He leaned back and let out a sigh of relief, before looking out at the distant exit of the tunnel. "The JSSDF is going to use an N2 mine any second now."

Misato recoiled just slightly. "What? You mean against that monster?" She looked towards the end of the tunnel. "They'd be crazy to just fling one at the Angel; it's a weapon of last resort."

The light at both ends of the tunnel then became intolerably bright for an instant, before a massive concussive shockwave shook the tunnel and the car inside. With it came the deafening roar of the detonation of the N2 mine.

The shaking was over soon as it began, and Misato held up her head over the undisturbed car's steering wheel. "Well… shit." She looked at Shinji. "Good call."

Shinji began to drum his fingers on the suitcase. "I knew it was going to happen."

Misato looked back towards the end of the tunnel. "I guess they would use it against a monster like that, huh?"

* * *

The Renault left behind in the parking lot, Shinji and Misato wandered their way towards the elevator. Since their descent into the Geo-Front, Shinji had grown more distant, a coldness wafting off him as he stared at all that his Father had spent the last decade or so building into a comprehensive fortress against the threat above. Misato had been keen to note that with their entry, he held tighter onto the case, reluctant to remove it from his sight.

"What is in that thing?" She asked.

"So this is what my Father has been working on…" He murmured as they meandered through one identical corridor after another.

"Ignoring the question I see." Misato gave the case another wary look. "Can you at least stop being so tense?"

Shinji took a deep breath, before steadily replying. "I've been called to a city being attacked by a giant monster they just blew up with an N2 mine, by my Father who just wrote a letter stating for me to 'Come'."

Under his breath, just within her hearing, he added, _"I've been unable to masturbate since."_

Some mental imagery was just too disgustingly powerful. His joke actually pulled a chuckle from Misato, as they approached the elevator. Before her finger could even touch the button, the doors opened to reveal an impatiently waiting Ritsuko clad in her one piece and lab coat. Shinji's aloofness immediately turned into tension, the leather handle of the metal case crinkling slightly as his grip became vice-like. Just staring at her, he suddenly desired causing her extensive physical harm.

A tense instant passed, as Misato's eyes widened in realization, but just as quickly, it passed. "Hey Ritsu-chan, sorry we got a little lost on our way here."

"It's alright, as long as you made it here. Is this him?" Ritsuko looked down at Shinji, wearing a mirthless smile.

Shinji looks back up at her. "Oh hello, you are…?"

He looked for a nametag, but only found glorious, grapefruit-sized breasts that seemed to strain against the fabric of her swimsuit. His eyes became stuck there, damn hormones, but imagining that his Father's probably been glomming all over them for years helped release him of their potent spell. Misato looked over at him, and then rolled her eyes.

"Doctor Ritsuko Akagi, Director of Project-E," she introduced herself; she had caught the little pervert's gaze sticking to her tits too. It could explain why he seemed so tense all of a sudden. "Did Captain Katsuragi give you your documents?"

Shinji held it up in confirmation and began to leaf through it as they boarded the elevator and it began its descent. "So, what exactly does Nerv do here? Why did my Father ask me to ejaculate?"

Ritsuko's brows went up, as Misato bit her lower lip to stifle another laugh. "Excuse me, Shinji?"

Misato held up Gendo's letter to Ritsuko's nose. At the Doctor's silence, Shinji let out a feeble sigh. "I'm allowed to be funny, aren't I?"

"Yes, you are," Ritsuko answered after a delay.

"Anyway, why am I here? Does it involve masturbation, because I could've done that back home."

"I hope that's not your only material, a mature sense of humor is preferred in the workplace." Ritsuko noticed the case. "Interesting suitcase, what's in it?"

"It's a suitcase nuclear bomb, six kiloton yield." Shinji didn't even look up from his booklet.

Ritsuko looked at the handcuffs connecting his wrist to the case, and raised an eyebrow. Letting out an amused snort, she dismissed his answer. "So you do have different material."

Shinji kept his nose in the booklet, as they left the elevator and walked onto another lift that took them upward at an angle, past a large tank of bakelite that glowed ominously and purple-y. As they ascended slowly towards its top, a voice called out from overhead speakers.

"All hands to battle stations. Prepare to intercept the enemy on the ground."

"That's serious." Misato looked towards the tank of bakelite, as they passed the sight of a giant hand frozen in the bakelite. "How's Unit-01?"

"It's configured with B-Type Equipment. It's being cooled," Dr. Akagi replied.

"What's the chance it'll work? It hasn't moved since we finished building it, right?"

Shinji flipped a page, as Ritsuko answered that. "The possibility of it working is zero point zero-zero-zero-zero-zero-zero-zero-zero-one percent."

"So it's a demon," Shinji quipped.

That threw Dr. Akagi off her game. "Wait, huh?"

"Nine zeros, oh-nine, oh-ni, oni, demon, right?"

Misato blinked, as Ritsuko remained off her center from that. "Ah… yes… that's exactly what we call the thing."

"Huh, I wonder what this demon called Evangelion is." Shinji's tone was just an edge sarcastic.

Ritsuko barely missed the cut, and something else. "Don't bother looking through the manual for it."

The elevator ride ceased, and the three left it in lieu for a boat ride across another purple lake, and from there they entered a dark cavernous room, plunging them into pitch darkness. Misato looked to Shinji, just as the lights came on, presenting the monolithic face of Evangelion Unit-01. She waited for his reaction, and when Shinji's brows merely rose, a red flag went up.

"So, you have a robot?"

Suddenly it was May Day in Red Square, as Misato took a step back from the boy and the coldness radiating from his tone made the cold liquid beneath them seem so warm by comparison.

"This is Evangelion Unit-01, the last great hope for humanity against the Angels, and you are its pilot," Ritsuko announced to the room, dramatic music playing in her head to go with it.

"Neat."

The record scratched, and it was Ritsuko's turn to plant a red flag on the top of Mount Consternation, as she slowly turned to face Shinji. This kid was downright _weird_.

Taking her silence as a no, while Misato continued to gape like a bass, Shinji set his case down, freed his hand from the shackle and crossed his arms. "So this really is all that I was brought here for?"

"That is correct!"

Shinji turned to face his Father, his eyes blotted by his bangs as he stared up at the man he had not seen in years. He looked so smug upon his perch, gazing down upon the Eva Cage floor like a king overlooking his perverse kingdom. The gleam of light off the rose-tinted glasses hurt his eyes as Gendo adjusted them before addressing his son.

"It's been a while, Shinji." There was a tone of indifference in his voice.

"Hello Father." Shinji's tone was laced with contempt.

Misato looked between Father and Son, and suddenly her shooting hand was feeling itchy.

Gendo smirked at his contempt. "Prepare to deploy in the Eva."

Misato looked back up at him. "Deploy, you mean Shinji, in the Unit-01?"

"We have no choice," Dr. Akagi said plainly. "Rei is injured and Unit-00's state makes it unavailable."

She then looked to Shinji. "Shinji Ikari, you will pilot it."

"Do I get a watch?"

Once again, Dr. Akagi was thrown off her game. "Excuse me, what?"

Ignoring her, Shinji turned and looked back at the Eva staring blankly at him like he was a next potential meal. "I really didn't want to believe it. I actually hoped things would be different."

He looked back up at his Father. "You only called me here, because you need me for something."

"That is correct."

A suffocating silence set in, only briefly, before Shinji's soft chuckle broke it. Gendo's eyes narrowed as the chuckle turned into a shuddering chortle that grew in volume before it became a hysterical laugh that would've made both Light and Iori Yagami cringe in horror like both Misato and Ritsuko were doing that very instant. His laughter tapering off, back into weak chuckles, Shinji slumped forward, his head bowed towards the floor.

Gendo did not expect this, and naturally he did not like it. Shinji looked up at him through his bangs, a deranged smile splitting his lips wide. "It's been almost a decade, wondering why you left me all alone and why you didn't want me. Now you come back into my life because you need me to pilot your piece of shit robot…"

"Shinji…" Misato raised her hands and took a step towards him.

Ritsuko was also concerned about the boy's mental state, what in the world happened to this kid?

"If you will not pilot, then I have no use for you," Gendo spoke, his composure still intact.

"Oh, I'll pilot, but on one condition," Shinji said his grin growing as he spoke.

Like his conditions mattered, however he would entertain the boy nonetheless. "And that condition is?"

Shinji reached to the back of his neck, near the collar, and began to scratch just underneath it. "I become the new commander of Nerv."

If he hadn't suppressed it with years of effort, Gendo would've laughed like his son had a moment ago, and likely then shot him in the face. The impudence of that boy, it was clear he was insane. "Doctor Akagi, prepare Unit-01 for Rei's use. Our spare is useless."

No one noticed the gleam in Shinji's eyes as Ritsuko and Misato turned to the Commander. "But Rei is still injured, you can't expect us to sortie her now!"

"She's still alive, all Unit-01 needs is a body inside of it to move," Gendo said before the gunshot rang out.

Stopping, the Supreme Commander of Nerv felt a burning pain in his gut, and looked down to see a single bullet hole in his torso that was beginning to leak blood everywhere. He looked towards his shooter, and grew wide-eyed when he saw Shinji aiming a compact pistol at him drawn from the back of his shirt.

Misato whirled around on Shinji, her own sidearm drawn in a flash as her shock was suppressed by her training. "SHINJI!"

She froze when he suddenly pointed the gun at himself and calmly asked. "Do you know what a Dead Man's Switch is?"

He was almost joyful as he kicked the case at his feet, unlatching it, his finger threading the trigger of his pistol as Nerv Section 2 likewise took aim at him, pistols trained on his heart and head. "They're triggers that expressly go off when the heart stops beating."

Misato looked from Shinji, and to the case, and dread washed over her. She lowered the pistol slightly. "No… no way…"

"Do you know what they're used for primarily?" He asked her, everyone in the room before using the toe of his shoe to flip open the case, revealing a most unpleasant device that made everyone lower their weapons.

"They're for bombs, in this case, suitcase nuclear weapons…"

He grinned.

"…Six kiloton yield."

Ritsuko leaped back, horrified. "Oh my God, oh my God."

Shinji looked up at his now trembling Father, who managed to remain standing despite his gunshot wound. "Oh, stop gawking Father! I'm pretty sure I missed your vitals with that shot, you'll probably bleed to death, but this is the last line of defense for humanity! It must have a modern medical facility, right?"

Gendo's jaw could not fall any lower. Somehow, his son had managed to sneak a nuclear device into Nerv, firearms as well! Why hadn't anyone checked him, or his belongings? Oh, yes, he never once thought Shinji would be capable of that. The scenario should've brought him a broken shell of a child, not an armed psychotic!

"What… what is your intention?" He demanded.

Tapping the pistol against the side of his head, Shinji laughed again. "Well, you see Father; after Mom died and you abandoned me I began having dreams, bad ones. They were about you, about Mom, a girl with blue hair, and a redhead that I just loved to _choke_. In all of these dreams, I learned things, things people aren't supposed to know and they made me a little _crazy_."

He scratched the side of his head with the muzzle. "Well, not crazy in the 'I'm going to start singing American Show Tunes while masturbating to kittens', sense. No, I've gone completely insane with rage, and you and Mom over there are both the most responsible for it!"

A nod to Unit-01 behind him caused Gendo's heart to clench in his chest. No, that was the pain from his gunshot wound.

Shinji continued, "So then, here's how it's going to go, Father. I'm in charge of Nerv from now on. Not you, not anyone else, me. And, if you don't like it then we can all go to Hell together."

He cocked back the hammer, terror filling the entire room. Gendo remained composed despite it. "You're bluffing."

Shinji stopped, and lowered his gun, it was pretty clear to him now that he didn't get his iron-balls from his Mother, that's for sure. He had to admit, that was damn impressive of his Father. Misato edged closer, ready to take Shinji down now that the gun was away from his head. She couldn't kill him, but restraining him painfully was a perfectly viable option.

"You're right," Shinji said. "It was a pretty good bluff, too. Thing is, if I wanted you dead, I would've aimed for your heart, or your head, or nicked an artery, or any of those things. I'm a dead good shot, you see, or at least my teacher always said so. Though I'm pretty sure if you did die, the only person who would really mourn you is the bottle blonde here that wants in your pants just like her Mom was."

Ritsuko felt the spotlight suddenly shine on her and she began to sputter. "W-what did you say?"

"Her mother, though, would be more than happy to see you drop into Hell. She's probably got a nice spot laid out in the lake of fire for you, too," Shinji added as he edged back from Misato, her movement noted from the corner of his eye.

A flash of light behind Shinji, Unit-01's eyes, made him smile. "It seems that someone is in agreement with me, eh Mom?"

Misato crept closer, the nearest person to him, and her entire body prepped for the lunge, she only had one clear shot at him. She cursed under her breath and froze, however, when he suddenly turned his attention to her, the ceiling overhead rumbling. "Damn it…"

"Your Angel is coming, Misato. Do you want me to kill it, or not?" He asked her.

"You didn't have to do this," She said back to him, her voice low and trembling with anger.

Shinji shook his head. "I had to, it's the only surefire way I'll get what I want."

"What do you want? What do you expect to accomplish with complete control over Nerv?" Misato asked with a frown.

Shinji gave her a dangerous look. "What do I want? You couldn't give me what I want. So I have to shake loose the people who have what I want and take it from them. What you can give me is what I need, right now."

He twirled the gun, and turned on the safety. "I need your help, and your trust."

There was another rumbling overhead, and Shinji looked up. "Time's running out for all of us either way."

Still unmoving, Misato was stunned as he had spelled it all out so plainly for her. This was exactly what he had planned for, putting himself in a position where they'd have no choice but to give him what he wanted. In a word, brilliant, and in another, terrifying, if she let him go, he'd be in control of the most powerful weapon Man has ever created, but it was exactly as he said.

"Prepare the Eva for launch, now!" she called out.

Gendo, his hand covering the bleeding wound as medical personnel reached him, grimaced in anger as the Captain gave in to his demands. The scenario was turned on its head.

As he watched Shinji stand down to board the Eva, a hilariously small part of him felt pride for his bold course of action. It was a brilliant, coercive maneuver that was so outlandish that no one, not even the MAGI, could've considered a possibility.

Pride that, ultimately, was snuffed out by insurmountable rage, his son would pay for this, the moment the bomb was disarmed, Shinji Ikari would rue the day he dared tried to challenge his Father's place. The boy was far too young to be walking so tall.

As Shinji walked past her, his head up and a perversely smug smile on his face, Ritsuko brought a hand to her chest and took a deep breath. She looked back after him, up to where his Father was being readied for movement to Nerv's hospital ward, and then down at herself. What the Hell just happened, and why could she not stop shaking?

"That was… incredible…" She uttered under her breath before looking back at Shinji in complete awe. "That was fucking incredible."

Quickly, she berated herself for loosening her façade and rushed to prepare Unit-01 for launch.

* * *

A/N: Now with better writing, more jokes, and complete and total coherence. Reload of ARSENAL will hunt down and murder its faults with the same glee as a black bunny rabbit!


	2. That's it, you're on my list

Disclaimer: If you're reading this, I'm-HNNNNNNNNNNNGH

**Reload of ARSENAL**  
That's it, you're on my list

_Shinji Ikari, the new HNIC_

**[2.]**

Curbstomp Battle: Slang, derived from the film American History X, defined as a battle, generally the victim of hype, between two equally powerful opponents that ends in a spectacularly one-sided manner. Example: The battle between the Third Angel, Sachiel, and Evangelion Unit-01 in the center of Tokyo-3.

From the moment it left the gates, Unit-01 dominated the Angel, breaking and tearing off its arms before crushing its legs and pummeling it into an unrecognizable mess of flesh, bone, and a shattered S2 core. When it was all over, there was blood all over the streets, buildings, and Unit-01, which sported not even a scratch for its trouble. Given the circumstances and its pilot, for the personnel within the Central Dogma, this was particularly disconcerting.

"E-Evangelion Unit-01 is… is…" Maya Ibuki murmured as the Eva seemed content with eating some of the remains of its kill. "N-Nevermind."

She needed to go cry, and she got up to do that. While Makoto Hyuga and Shigeru Aoba silently tried to wrap their heads around the violence they had witnessed. Behind them, Ritsuko was still struggling with the sudden crush of events that came with the Third Child's arrival and his coup. On one hand, he was dangerous beyond measure, but on the other hand he got results.

Then there was the fact that she was incredibly attracted to men with power, and Shinji had displayed enough confidence and swagger in his grab for it to convince her that maybe it was something in the Rokubungi gene pool that made them naturals at getting women inappropriately aroused.

This blossoming attraction was no small influence on her conflict, as she found herself wondering what she would do if Shinji did gain control of Nerv, and how much she would enjoy it if she played her cards right.

Misato was already waiting in the cages for Shinji's return, along with two platoons of JSSDF Soldiers and Nerv's own internal security force. When Unit-01, restrained and unpowered, slid down into its gantry, guns of all varieties and caliber were trained upon the cowling that protected the entry plug. Inside, Shinji lounged in his seat with his hands folded over his waist, not at all surprised by the "Hero's Welcome".

With a hiss and groan, the Entry Plug was drained, extracted, and automated commands opened it for Shinji to find Misato waiting on the edge of the catwalk, with at least six JSSDF soldiers all aiming rifles at his face and neck. Her own pistol ready, she trained it on Shinji as she stepped closer.

"Get out of the Entry Plug with your hands up and out. If you comply, you will not be harmed," she spoke to him, all business in her tone.

Shinji did as told, climbing out of the plug and onto the dry catwalk before spreading his arms out. The fear in the room was palpable, as if they were expecting him to conjure up an AT-Field and go to town on them. Man wouldn't that be awesome? Shame he was just a normal boy outside of his majestic monster of a robot.

"I don't have your trust yet, do I?" He complained to Misato, before addressing her backup, "Do you really need all this help taking me into custody?"

"Do I?" Was he going to make this harder for her? Shinji scowled.

"Right now, you have specialists working to disarm Hiroshima-kun with the help of the MAGI." A beep sounded from his pocket, and Misato could see the edge of a smart phone sticking from it. "And there it goes. Well played, Father, you ran a tight ship."

Misato didn't like that he wasn't concerned. "You planned for that, didn't you?"

"I expected that you would disarm it, this is the most advanced military organization on Earth," Shinji replied to her. "Do you play Shogi? Chess? In those games, you have to plan your moves, calculate your gains and losses and use both to further the ultimate goal."

"So losing the nuke is part of your plan."

"I can afford it, I have more than one suitcase nuke."

Misato's breath left her in a long wheeze. "What."

"I have more nukes, hidden somewhere in the city. After the Second Impact, Russian-built suitcase nuclear weapons the GRU placed at their predetermined deployments were lost due to the anarchy. GRU Agents, some of which were inducted into Section 2 after Gehirn's reorganization into Nerv, had managed to reacquire some of them to sell illegally to whoever wanted them. I had managed to get a hold of one of those agents, and he had a fantastic stockpile of eight in total, ready for sale to any bloodthirsty maniac who wanted a bit of power at his disposal."

He pointed to himself. "He gave them to me, and they are all connected to my Dead Man's Trigger."

Misato's hands trembled. "Where are they?"

"I won't tell you. I need those to make sure people don't get the idea to knock me off, they're my insurance policy until I convince all of Nerv to accept me as their leader."

Misato grabbed his collar, yanked him close, and placed the barrel of her pistol against his chin. Shinji blinked, and stared at the gun before looking at glowering face. Briefly, fear of mortality bubbled up, but he repressed it as he returned her stare.

"What are you going to do when you have control? What can you do that your father already isn't doing as Commander?"

Shinji answered. "I'll tell you what I won't do. I won't turn around and wipe out the rest of mankind in some grief-driven delusional effort to reunite with my dead wife, like he intends to."

"What are you talking about?"

"It's my father's goal for Instrumentality, to use Unit-01 to trigger the Third Impact and reunite with my mother."

At Misato's disbelieving look, Shinji continued, "It's why he chose me to be Unit-01's pilot, to be his unwitting pawn in the scenario."

She tightened her grip on his collar in response. "I don't believe that."

"You have every right not to, all you have to go by is my word. But I'm telling you the truth, the dreams all end the same way and they haven't been wrong yet. I know what his plans are." He pointed at the cross that hung around her neck. "Just like I know your father gave you that cross, when he dropped you in that escape capsule during the Second Impact."

Misato dropped Shinji and took a step back. She stared at him, as though he had become an Angel right in front of her. She looked down at the cross, and then back at him. She hadn't told anyone exactly how her Father gave her the cross. No one else could've possibly known that, not even Kaji.

"Captain Katsuragi…?" One of the soldiers asked as she suddenly holstered her pistol.

"Stand down!" Misato ordered, before she grabbed Shinji again. Quietly, she hissed to him, "How do you know that?"

"I already told you, the dreams haven't been wrong. I can tell you more, but I need your trust."

"And how do you know I won't betray you the moment you've told me anything?"

"Because if you were that kind of person, I never would've told you a thing if I had no reason to trust you," Shinji said as he reached up and grabbed her arms. "Besides, you want revenge against the Angels, don't you? I can give you that, and revenge against the people who caused all of this to happen too, including my father."

"What do you mean by the people who caused all of this?"

"Do you really think this ends at my father? His version of Instrumentality is just one of two scenarios."

Misato's eyes widened. "…The Committee?"

"I have a list of names of people who all have their hands in the cause of the Second Impact, and are all currently working towards triggering the Third Impact so they can control Human Instrumentality to gain the power of God."

He tightened his grip. "The Human Instrumentality Project Committee and Gendo Ikari killed your father and billions of people to get this far, and they're now ready to use you, me, and everyone in Nerv to achieve their ultimate goals. Two Billion obstacles have been removed and fourteen remain–thirteen as of my battle with that Angel."

Misato released him, her entire body numb. Internally, she was wrestling to denounce him on the spot, but she couldn't bring herself to. No, there was just no other way he would know, they had just met.

"Oh my God… y-you're telling the truth," she whispered back, her voice shaky.

"Captain, what's the matter?" The soldier called back. When the boy had begun talking specifically to her, everyone in the room grew concerned by her reactions.

Misato looked back to them. "Lower your weapons and stand down, that is an order!"

The soldiers stopped. The same soldier spoke out. "What? But our orders from the Sub-Commander were-!"

Shinji snorted.

"I said, stand down!" She turned back to Shinji and slowly picked up her pistol. "I swear to God, if you are only doing this for your own selfish agenda, Shinji Ikari I will kill you on the spot. Do I make myself clear?"

"Do I have your trust, Misato Katsuragi?" He asked, plainly.

Closing her eyes, Misato slowly nodded. "For now, yes, you do."

Shinji smiled to her. "Then it will be unwavering."

Again, Misato nodded. "Now, tell me. Did Gendo leave me and my father to die there in Antarctica?"

Shinji nodded. "Yes."

"What of Sub-Commander Fuyutsuki?"

"He is on the list, but a lesser evil. I need him," Shinji replied.

Misato looked aside to the hesitant soldiers, resolution blooming within her. "This is a heightened alert! As of this moment, Nerv is to initiate a state of lockdown and Gendo Ikari and Kozo Fuyutsuki are both to be placed into custody immediately!"

Shock enveloped the soldiers and personnel, as Ritsuko arrived on the scene. A soldier immediately called out. "Under whose authority, Captain?"

Misato thought quickly. "Under the authority of the UN, now do as you are instructed immediately! Go! Go! GO!"

Her anger was stifling, almost robbing her of her rationality as she stormed down the catwalk towards where Ritsuko had emerged, Shinji in tow. One of the soldiers, noting this, raised his rifle. "What about the Third Child?"

"He is in my custody!" Misato snapped as she grabbed the soldier and shoved his rifle aside. "And he is not to be harmed, is that clear? Now stop standing there like a moron and do as you have been instructed, soldier!"

Panicking, the soldier quickly nodded. "Y-Yes ma'am!"

Misato looked back to Shinji brandishing her pistol. "Come with me, we're going to have words with ex-Commander Ikari."

As everyone seemed to run around in a panic of a most fearsome Captain Katsuragi, Shinji again could not help his smile. It would not be long now, before it was all his.

First things first, it was time to check on dear Father to see how he made out from his shooting. When the two of them walked past her, he cast a look to Ritsuko, who shared the wide-eyed expression of all the others along the catwalk, and winked to her.

When he passed, Ritsuko looked back after him, and felt her knees grow weak.

* * *

The bullet wound, as Shinji had so proudly stated, was non-fatal. Despite being fired from long range at an angle, it had passed completely through Gendo while missing his internal organs and vital arteries. That did not make it any less painful, in fact, it hurt like a motherfucker even more when he realized that his son was an excellent shooter and this had somehow escaped his notice.

Section Two had been blinded, and when he found out by who, he was going to punish them swiftly.

When the door opened and Shinji walked in with a brooding Misato, Gendo immediately realized something was wrong. The Third Child wasn't in jail, and Katsuragi looked like she was about to choke a bitch; that her glare zeroed in on him made his dread all the more palpable.

"And the meaning of this is?" He asked, looking at both with an unmoved expression.

"Ikari Gendo," Misato said to him, "I have arrived here to officially place you under arrest."

Silence reigned, Gendo looking at Misato with an utterly shocked expression. "What do you mean by 'under arrest', Captain?"

"For treason against humanity, by willfully colluding with individuals who seek to initiate the Third Impact and utilizing UN appointed and funded resources to achieve that goal," Misato answered.

Gendo's eyes widened slightly, before he looked to Shinji. "You did this, didn't you?"

"Yes, I showed Katsuragi-san the truth, and now she will help me in Nerv's restructuring, starting with a changing of the guard type thing," Shinji said with a smile.

"I see. Captain, what proof does Ikari have for any of his claims being the truth? How do you know that he is not being a madman as his previous actions have indicated?" Gendo asked, conversationally.

Drawing her pistol, Misato pointed it at Gendo, her eyes narrowing as she placed Gendo's face right in her sights. "Irrefutable proof, Shinji has told me things in no way he should know."

"They're the delusions of an angry child," Gendo dismissed them.

Misato reached up to grip her cross in her free hand. "No… there are just some things no one could possibly know."

"So you would execute me here, on the word of a child who has taken this entire facility hostage with nuclear weapons?"

"No… I should execute you for killing my Father, my friends, and so many other people, Ikari." She cocked the hammer and squeezed the trigger.

The shot never came, as Shinji placed his hand on the pistol and pointed it away from Gendo. Surprised by his sudden intervention, she looked to the boy. "Shinji…?"

"Killing him now will not give either of us any satisfaction. The ex-Commander is much more valuable to us alive." Shinji smiled to her, an expression that grew markedly sadistic that she read plain as day, seeing the smile's metamorphosis immediately brought Gendo to perspiration.

Misato nodded to him her own unpleasant smile forming. "Oh no, I wasn't going to kill him now, Shinji. _Ex-_Commander Ikari is going to be confined to a hospital bed for a while due to his serious, serious injuries."

"Serious? What happened?" Shinji asked, with mock apprehension.

She looked back at Gendo out the corner of her eye as she opened fire, the gunshots tearing into both his arms near the shoulders. Turning to face him fully as he stared back at her in muted agony; she pointed the pistol at his left knee and fired twice, shattering his kneecap.

"Some clumsy woman's gun went off, and broke his leg and shoulders. A weapons malfunction, but at least he was close to the medical ward when it happened," she explained to Shinji.

"Oh, I see. That is awful! Someone will have to take over for him while he recovers!" Shinji exclaimed.

He looked to Gendo. "I guess I'll nominate and instate myself as the new Commander. There, now there's no problem at all."

Once again, Gendo's ten-ton balls came into play. Despite his horrible agony, he looked his son right in the eye, and adjusted his now blood-stained glasses… with his middle finger. "Your impressive displays will get you only so far. Your resolve will wane, and then you will be crushed."

Misato, not at all surprised that the man could maintain such composure after being shot, walked over and pressed her gun in his face, snatching off his sunglasses as she did. "I swore to kill those responsible for my father's death, and I have six rounds left."

"Consider yourself lucky, Father, my Captain is showing a disproportionate amount of restraint by not killing you right now. But don't mistake mercy for weakness; she will fulfill her vow, just like I will mine to take care of you and all of your accomplices." Shinji patted Gendo on his good leg as he scooped up the sunglasses off the bed. "You get well soon now, okay Father?"

He got up, turned around and walked for the door, his face a mask of disgust from just touching him. "Shoot his other leg out."

"With gusto." Misato got up and fired twice more; tearing apart Gendo's other knee before shooting his dominant hand for good measure.

Satisfied, she followed Shinji out and past the shocked doctors and nurses who stood gathered around the doorway. "Don't just stand there, treat his wounds and make sure he's well restrained. Now go."

As she left them to work and followed Shinji, Misato briefly wondered if she were going insane, before she decided that it did not matter. Everyone here at Nerv already had some weird issue, and now it appeared the new self-appointed Commander Ikari was going to be hard at work turning this entire operation inside out… messily.

Bleeding from multiple, severe wounds, Gendo appeared strangely serene as the medical personnel rushed to his aid, before his mangled shoulders drooped and he let out a loud, bellowing roar. He did not scream from the blinding pain of his injuries, it was the striking realization that his scenario had, in the course of only a few hours, crumbled into nothing.

* * *

Outside the room, Shinji slumped against the wall as he heard his Father's telling scream. Misato was at his side immediately as he slid down to sit with his back against it. "Shinji, what's the matter?"

Shinji looked up at her, his face serene from the release he had experienced. To her surprise, however, she could see the sadness radiating off him, why?

"I've waited and planned for years to do this, Misato. I had to hide every movement and plan for every single contingency, do you have any idea how much this anger has eaten at me?"

"Shinji…" A strange compulsion roused her, and she leaned forward to hug him, which he returned tightly as he let out a long sigh. It felt natural doing this, and déjà vu washed over her, like she had done this before, in another life. She squeezed him a little tighter.

"Let's go meet with Fuyutsuki, then. I promise to be a little more civil," he said as he pushed her away to get back up.

She helped him to his feet. "More civil, you say?"

"He's a lesser evil, but a necessary one for what I need," he answered; he appeared much less manic now that his Father had been dealt with.

However, when both turned to find a more properly dressed Ritsuko standing before them, anger returned to give his features slight color. "Hello, Doctor Akagi."

"Hello, Shinji." She was understandably wary of him; she had clearly read the subtle changes of his expression when he turned to her, as had Misato.

She looked at the glasses he held in his hand, and then between him and Misato. "Nerv is in chaos, no one knows what's going on, and Section 2 is telling me that you ordered Fuyutsuki and Gendo to be put under arrest. As the Director of Project-E, I'm third in line under the command structure, but I've been told nothing since you ran off with Shinji. What is going on here, Misato? Where is Commander Ikari and what's his condition?"

"Gendo Ikari is no longer in charge, I am," Shinji said as he held up the glasses, before dropping them to the floor and stepping on them. "The scenario has been changed, there is no more scenario, there is only ensuring that the Third Impact and Instrumentality does not occur, under any circumstance."

Ritsuko looked to Misato with wide eyes. "You're with him on this?

"Yes," Misato answered bluntly, causing Ritsuko to turn her attention back onto Shinji slowly.

"He… he… you are in charge?" She asked him. "For what reason should I even acknowledge your leadership then, Shinji Ikari?"

Shinji's smile slowly returned as he answered Ritsuko's stare with his own, and she froze like a mouse in the eyes of a snake. He stepped closer to the woman and brought finger and thumb to her chin, capturing it and pulling her face close to his.

"You're attracted to men with power, aren't you?" He asked.

Ritsuko's face colored, and she quickly swung her hand to slap him. He caught her hand before it reached his face in a grip much stronger than she expected. "It's why you lust for my father, isn't it?"

At her spellbound look, he clarified. "Yeah, I know."

He pulled her hand away from his face. "I'm not my Father; I'm younger, better looking, and far more powerful than he ever will be. I'm the only one who can pilot the Eva, after all. What reason would you have to not acknowledge me?"

Releasing her hand, he stepped inside her personal space. He rested his hand on her cheek, as he stared her down once more. "At the very least, I won't say 'Yui' when it counts."

He drew his hand away, caressing her down to her cheek as he walked past her.

Misato was now completely dumbfounded to the point of numbness; Shinji's limitless explicitly was wholly baffling. She turned to Ritsuko, and her numbness turned to horror that chiseled itself into her visage when she saw that her long time friend and co-worker was not shocked or angry, but staring at Shinji visibly aroused, her face flushed, hand on her chest over her rapidly beating heart, and her breath coming out in soft, rapid pants.

Shinji called to Misato from the end of the corridor. "My office is this way, right?"

Before Misato could answer, Ritsuko spoke up, her tone completely changed. "Yes, wait for me Commander; I'll take you right to it. I have a report to issue anyway on your battle with the Angel."

"Excellent!" Shinji returned, happy to have earned his second follower.

She still had a few rounds left, she could kill Ritsuko right now, Misato thought. As Ritsuko took a step towards Shinji, Misato grabbed her by the shoulder and whirled her around to face her before grabbing both of them. Her face was a mask of gravity and death as she stared down the Project-E director.

"W-what?" She asked.

"Ritsuko, why are you staring at him like he's a piece of meat?"

"I am not!"

"You're soaking through your panties."

Indeed, Misato could look down and see the hints of arousal running down the insides of Ritsuko's thighs. Ritsuko grew indignant, puffing her cheeks. "Okay, so I am? It doesn't mean I don't have a report to give."

"Don't you find jumping from one Ikari's cock to another morally reprehensible at all!?" Misato sure did, and anyone with a degree in common sense would agree with her.

Ritsuko pulled away and turned to walk down the hallway, only pausing to look back. "Misato, I'm going to ask you very slowly. Are you questioning the morality of my seducing a terrorist who just an hour ago threatened to kill us all with a nuclear weapon?"

"Yes!"

"Are you questioning the morality of my seducing a nuclear armed terrorist whom you just assisted in taking over the entirety of Nerv?"

"That's not my point…"

"Are you questioning the morality of my seducing a nuclear armed terrorist whom you, without hesitation, followed a direct order from to shoot his injured father with intent to further grievously wound?"

Misato was silent.

"I thought so." Ritsuko went skipping down the hall. "If you need me, I'll be under Shinji's new desk~."

"God damn it, Ritsuko…"

The doors to Gendo Ikari's former office opened, and Shinji walked in with Misato and Ritsuko in tow. A great expanse of bare, dark room with walls, floor, and ceiling all black, and devoid of furniture save the desk and chair near windows currently shuttered. The tree etched into the ceiling was a tad gaudy, it would have to go, as would everything else…except for the desk, he kind of liked it.

"Nice," Shinji said as he ran his fingers over the wood surface in his stroll around it to the chair. He took a seat, and immediately propped his shoeless feet up on the desk, toes wiggling inside his socks as he sank into the chair. His father sure knew style; he'd give him that as well.

The drawers on his side of the cabinet were all easily opened and explored. Inside he found what he'd expect, a handgun with ammunition and magazines, a few photographs of Yui and himself, official documents filed under "pretend to give a shit but really don't", a few photographs of Rei after her nasty accident, and finally the prize of his search. He leaned back into his chair, feet up on the desk again, and opened the wire-bound notebook he had absconded from its place of storage.

"What is that?" Misato asked.

Ritsuko walked over to the desk, under the other woman's hawk-like gaze, and stood beside Shinji. He regarded the Doctor with only a glance before flipping a page of the book. "It's a log of his personal thoughts. Oh, what's this? A rough draft of the letter Father sent me."

"Oh?" Misato folded her arms.

Shinji began to read it, his expression darkening. "He put so much thought into this; he even said he was sorry a few times."

Misato grimaced in disgust, while Ritsuko offered an explanation, "I imagine he wrote it to get his feelings out of the way. I suppose even Gendo has his insecurities."

"A whole journal full of his true feelings, that's almost worth sympathy, almost." Shinji picked up a lighter from the drawer, flipped it open and set alight a corner of the journal before tossing it over his shoulder against the wall to burn.

The doors opened, and Fuyutsuki walked in to the sight of Shinji sitting at Gendo's desk, Misato standing passively before it, Dr. Akagi next to it, and… was something on fire? Frowning considerably, he approached the desk, joining Misato's side. "Shinji Ikari."

Section 2 had delivered him right on schedule, Shinji smiled to him. "You're not going to fight me on this too, are you Fuyutsuki-sensei?"

Kozo Fuyutsuki was a shrewd, well learned man, with a degree in Having Half a Brain and a PhD in Common Sense. Therefore, when faced with a violent maniac who usurped the control of his military organization around him in less than an hour, he acted appropriately. Ergo: He went along with it, to see where it was going. Shame he could not impart this lesson onto his now severely crippled pupil, but oh well.

"It's been a while since I've been a teacher," he said to Shinji calmly.

"Well, consider this your first assignment; I need to know everything about how this base is run, nouns in particular," Shinji explained bluntly, his nose twitching from the irritating smoke behind him.

Fuyutsuki managed a humorless smile. "Are you sure you wouldn't prefer shooting me as well? If you know about Gendo, then you know about me."

"I need you around because you still have a shred of human decency left in you. Kind of like what my Father needed since he wrote all of his off in that little notebook of his."

Shinji waved his hand by his mouth derisively. "What a loser, am I right?"

"It was a habit of his since college; you should see some of the things he sent to Yui that she left with me."

Shinji blanched. "I'd rather not; the one love letter to me has scarred me for life."

"Very well, so what do you need from me other than my 'shred of human decency' and my knowledge of Nerv's operations?" He asked.

Shinji laughed again, gaily, before he violently slammed his hands on the table, causing Ritsuko and Misato to jump. His demeanor had suddenly changed, becoming deadly serious. "I'm exterminating The Committee, and I need you to get to them."

"I can't see why you would, The Committee will find out about this situation soon enough. It'll be impossible for them to not."

"I know they will, and when they do, they'll do everything in their power to stop me, which is why I need you," Shinji replied. "As long as there are Angels, Nerv is needed, once this organization has served its purpose…"

"They will eliminate us," Fuyutsuki finished.

"The Committee will know that Gendo is disposed and I'm running things. What they need is misdirection and misinformation to keep them from suspecting that I'm after them next until it's too late. From here on out you will tell them what they want to hear," Shinji replied.

"With no change of our modus operandi, I assume?"

"Precisely, well, aside from a few projects."

The humorless smile remained, as Fuyutsuki nodded. "Understood, I will take my post immediately. What shall I tell The Committee of Gendo's disposal?"

Shinji raised a finger to his chin thoughtfully. "Hmm… tell them that he fell down an elevator shaft."

"Onto some bullets, I presume?" Fuyutsuki's dry response drew a sharp, manic laugh from Shinji that caused Misato to close her eyes and remind herself quietly, repeatedly, that this was for the good of humanity.

"No, that I pushed him down one because he's getting in the way of Grandpa's plans."

Fuyutsuki's brows rose in surprise. Reaching to The Committee to get close to them was both dangerous and brilliant. They'd never trust him, but if he removed Gendo from the equation for them, and played closer to their scenario, then he had his foot in the door at least. At any rate, he doubted he was going to get out of this alive.

"However, you try to sell me out and you'll be in worse shape than my Father is, got that Fuyutsuki-sensei?" Shinji said as he dropped back into his chair.

Fuyutsuki nodded. "I will make a note of that."

Shinji beamed and made a shooing gesture. "Good, now get out of my sight."

The impudence of Shinji's tone actually ate at Fuyutsuki less than Gendo's monotone arrogance. Perhaps it was because he saw it for what it really was, or because he truly disliked his student, but his smile became a bit more genuine as the old man nodded and excused himself.

Naturally, the overtones were not lost to the others in the room, but for Misato grasping it was out of reach, she was of course more surprised that Fuyutsuki in no way protested this violent takeover. Was he planning something? The old man was supposed to be cunning in his own way; it was why Gendo chose him as his second-in-command.

Ritsuko was on a wildly different wavelength altogether, a long, bone-deep shiver ran through her body the very second Shinji had ordered Fuyutsuki out of the office. It went without saying that the good Doctor was now unashamedly basting in her own juices, and Misato was ready to stick a fork in her. Forks. Forks with tungsten tips.

"I feel kind of bad, talking down at him like that," Shinji said suddenly, catching the attention of both. "But then I remember he wants what they all want, just with different ideas on how it should happen."

"So, what do you want, Commander?" Ritsuko licked her flushed lips slowly, and swallowed.

"That none of them get what they want."

Misato nodded in agreement, and felt a little more confident with the overtone of his statement. Ritsuko only again shivered in delight, and it did not escape Shinji's notice.

He frowned; it was time to put this one in her place. "Misato, could you step out?"

An electric shock went through Ritsuko, and Misato raised her hand in protest. "Shinji, I don't think that's…!"

Shinji gave her a pleading look. "Please, Misato?"

She stopped at that, and with great reluctance she stepped to the door, her eyes not leaving Ritsuko until the door shut behind her. The other woman watched the door close, and turned predatory gaze to her new Commander as she licked her lips in anticipation.

Shinji stared impassively back, issuing his challenge.

"So then, _Commander_…" She walked to the desk, and boldly climbed onto it directly in front of Shinji, sitting on the edge as he pushed himself back from it, and spreading her legs partly. Naturally, he looked down and his face turned a light red. "What would you like for me to do for you?"

"Issue your report," he replied as he looked up from the obvious fact that Ritsuko forgot underwear when she dressed.

Ritsuko just smirked and, ignoring his request, she slid down from the table and to her knees in front of him. She looked up to his face briefly, before she looked downward, her hands seeking to undo his pants.

Cold steel rested against her forehead the second his fly was undone. She looked back up at him, and the pistol he held to her head. "You're on the list too, Doctor Akagi."

She just smirked and replied, "I figured."

Ritsuko proceeded to deliver a different kind of oral presentation.

Shinji did not pull the trigger.

Damn hormones.

* * *

A/N: Damn hormones, indeed!


	3. Free Agency

Disclaimer: It would appear that people would find my death to be "awesome". To anyone who wants me dead, _come and get me!_

**ARSENAL**  
Free Agency

_Whether it's finding a good job or saving the world: It's not what you know but who you know._

**[3.]**

Here they were again.

Instrumentality had come and gone. The world was lifeless and still, the whole of humanity lay in its grand final form–a primordial soup locked in the never ending bliss of unexistence. Not a single living soul remained, except for Shinji Ikari–whose hands were clenched tightly around Asuka Langley Soryu's throat.

It was happening again. Just like last time, and the time before, and the time before, and the time before. No matter what he did or tried, it just kept happening. The fear, the hatred, the loneliness never stopped. Here he was again, on the precipice of the climax. He had to stop it, the one thing he could stop. He didn't want to hear it again.

She reached up and caressed his face, and his grip went slack. Resignation washed over Shinji, as he let go of her neck, and let his face drop down to rest against her chest. His eyes clenched shut, he began to sob weakly, as Asuka rested the hand of her maimed, bandaged arm atop his head.

He couldn't change anything. The outcome was always the same. Staring up at the sky Asuka uttered the words he dreaded, but had come to accept as an inescapable truth.

"How disgusting."

Shinji Ikari, six years old, opened his eyes and stared up at the familiar ceiling of his guardian's home, as he had come to do hundreds, thousands, maybe even millions of times by now. Sitting up, the child picked up a journal resting on the nightstand next to his bed in his dull, sparse bedroom, and opened it. Written all over the pages were lines and lines of pure madness. Verbatim recordings of his dreams, written over and over at the frequency they repeated. He was on the last page.

"I can't do this anymore," he said of the journal, the latest of dozens he'd filled.

It had been almost three years, since just after his mother's death, that he'd been having the dream almost every time he slept. It was the same dream, a long, unending stream of consciousness from the moment he first arrived at that place, Tokyo-3, to the inevitable conclusion on the beach at the end of the world.

For most of the dreams, it was through his own eyes, but sometimes he could see it through others–people that knew the Shinji in his dreams, and sometimes people that he'd never seen at all. It was to the point that he knew each and every character by heart, as if they were him. No matter what he saw or how he dreamed it, however, the events were always the same. While at first the dream confused and terrified him, after three years of unceasingly dreaming the end of the world, Shinji understood its meaning exactly. Today, he was not going to start another journal. Today, he was going to act.

Getting out of bed, Shinji cleaned up and dressed for school, before he left with a polite farewell to his guardian. The relationship between Shinji and the teacher who Gendo abandoned him with was impersonal from day one, and only more distant as Shinji began to dream and understand it. Naturally, he didn't tell his guardian of his dreams–his next guardian, however, would get a full disclosure.

As with most days since his abandonment, Shinji left his home and began walking down the street towards his school. He distanced himself from the other children, as usual, focusing entirely on the path in front of him and the music streaming through the earbuds of his SDAT Player. However, as he reached the front gate of his school, he walked right past it and kept walking. He didn't really need school anyway, everything he knew was more than enough.

From the time SDAT's tracks went from the first to the twenty-sixth, he was outside the small town he didn't even care to remember the name of, walking alongside an almost empty road. Almost, for a black sedan that had come around the bend ahead slowed down as it approached him. Glancing back, he watched the car pull over to the shoulder and come to a stop behind him.

Shinji turned to face the car as the doors opened, and a pair of men in black suits with black ties and black sunglasses emerged from the car. The man from the driver's side closed the door, and walked over to him. "Shinji Ikari, we're here to take you back home."

Shinji nodded. "You are Gehirn Department of Security Intelligence, yes?"

The two agents abruptly gave pause, taken by surprise. Shinji nodded again. "Didn't expect me to know, did you?"

This kid was creepy, Agents Andrei Rohmer and Pavel Korolev immediately thought. They had no idea what they were about to find themselves in.

* * *

In the present, Shinji sat back in his new chair in his new office, staring up at the complex diagram etched into the ceiling. Part of him still could not believe it was actually happening; he had the Eva, he had removed Gendo, his takeover of Nerv was almost complete. So far, so good. Not good enough, though. Time to get back to work.

"Hey, where do you keep Rei?" He asked Dr. Akagi as he tapped his pistol against the top of Dr. Akagi's head.

The doctor looked up from her oral presentation. "In an emergency sick bay near the Eva cages, we were keeping her there-"

"In case I didn't want to pilot. The Commander wanted wheel her out and let my empathy force my hand," Shinji said as he prodded her cheek with the barrel of the pistol.

Dr. Akagi nodded. "You've read your father's book."

"I've read all the books," Shinji replied. "I want to go see her."

Dr. Akagi nodded. "As you wish, Com-mph…"

Shinji had forced her head back down with his free hand. "After you're done, Doctor."

Not long after, Ayanami Rei emerged from a drug-induced stupor and stared at a familiar ceiling. Something was wrong, and while she could not understand it all for her lack of infinite wisdom and all-knowing, she felt a nagging intuition that it was something serious. On the other hand, she felt… good. Yes, good was a perfectly fine way of describing how she felt, she was not a girl with storied volumes of synonyms. Had Rei been a girl of more liberal conventions, she could describe it as "Fan-fucking-tastic".

A painful jab in her arm alerted her. Scanning the room with her unbandaged eye, Rei's gaze came to rest on Shinji and Dr. Akagi, the former fondly smiling upon her. "Hello, Ayanami."

Rei stared at him long enough to blink (wink?) twice. "Third Child."

She wondered what the Third was doing in her hospital room. Did he pilot the Evangelion as the scenario demanded? Well, they weren't all dead, so it had to be the case, any hard scrutiny was honestly lost in the painkillers that allowed her such comfort.

Shinji was completely mesmerized. Even wrapped in bandages, actually seeing Rei in person was as amazing as it was chilling. He, the trigger-man on the gun pointed at the human race, was staring directly at the trigger… and she was beautiful.

Okay, that may have been his heretofore unnoticed fetish for bandaged girls flaring to life, but he did appreciate the artistry that went into making her. "I'm glad that you're doing well, Rei."

Rei stared at him, not feeling particularly compelled to thank him for his concern. Her drugged-up brain was still trying to turn over why he was here specifically. She turned her gaze to Dr. Akagi, hoping for some kind of explanation, but only got a look of mild contempt hidden behind a veneer of faux-professionalism.

She didn't need to look to the Doctor for answers for long, because Shinji was more forthcoming. "I wanted to tell you, that I've taken control of Nerv away from my father."

Gears worked, as she tiredly processed the information that Shinji had given her, this was not in the scenario. She looked down at herself, at her hands, and stared at them. When she moved her good hand, her good eye widened and followed it, what a bizarre effect yet at the same time engrossing.

Noticing this, Shinji tried not to bury his face in his palm. Ritsuko must've given her an extra dose of painkillers, wonderful. He had to admit, she was very cute looking so lost.

She finally spoke, her tone a little slurred but still the same, quiet girl from his dreams. "What has become of the Commander Ikari?"

"He's being put in the deepest hole I can find, for what he wanted to do to the world. I don't want Instrumentality to happen."

Rei fidgeted, and wondered where that dragon came from. "You have no faith in your Father's work?"

"I do, but up to a point."

She ignored the dragon, and the arrival of Freddie Mercury to do battle with it using the power of rock. "What point?"

"I was with him up to the point where he wanted to kill every single person on the planet, so he can be back with my mother."

Rei nodded. "Then… what is my purpose?"

He reached forward, and rested his hand on her face, and she froze, struck by the clarity of his eyes as he saw back into her with the same unintentional intensity she regarded for others. She uttered a soft sound, part mewl, part whimper as he leaned closer to her. There was a tightening in her chest, new and utterly frightening to her, as he caressed her cheek, and brought his free hand to the other side of her face, touching and appraising her like she was fine china.

"Your purpose now is to save mankind now from the Angels and from anyone who desires Instrumentality, Rei Ayanami," he said.

Rei stared at him, and she grew anxious despite the narcotics in her system. Shinji could see the conflict waging behind her red eyes, and rested his forehead against hers as he stroked the top of her head. He took care to avoid her bandages, as he luxuriated in the feel of her strange-colored hair.

Rei mewled again, and closed her eyes. Her heart was racing now from the soothing touch. "Ikari…"

"I'm your Commander, now," he whispered back.

Taking several deep breaths, Rei struggled against the alien feelings he had suddenly triggered. Not only in his words, but in the way he touched her with such intimate familiarity. However, the warmth and haze won out, and Rei relaxed against him.

"I will serve you, Commander. What are your orders?" She spoke, a tone quiet even for her.

Shinji's lips curled into an anticipating smile. "Smile for me, Rei."

What a strange request, but she honored it nevertheless, the corners of her lip pulling upward just so slightly into a small, unexpectedly inviting smile.

To her surprise, Shinji closed the distance between the two of them to kiss her deeply. She froze immediately, eye wide, but protested not at the alien sensation of his mouth over hers, or his tongue exploring its recesses for only the briefest moments before he pulled away.

He had always wanted to do that. As Rei stared back at him, devoid of even the beginnings of a response, he ruffled up her messy hair and stood up. "Well, you focus on getting better, okay? I'll see you later."

For lack of a better reaction, the wide-eyed, brightly blushing girl just nodded. "Understood, Commander."

Shinji smiled, and all but floated out of the room, his footsteps were so light. He stopped floating when he found Misato waiting with her arms folded.

"And what was Rei's original intended purpose in the Instrumentality Project?" She asked as Dr. Akagi joined them.

Shinji seemed almost nonchalant. "She's the trigger."

Misato recoiled. "W-what?!"

"Yes, we even made clones of her in case something happened to her," Dr. Akagi revealed nonchalantly. "This Rei is technically the second."

"What happened to the first?" Misato looked a bit ill.

"My mother killed her, before she killed herself." Ritsuko's nonchalance was beginning to seriously get to Misato. Before she could say something, Shinji grabbed the raven-haired woman's arm.

"Rei was just as much a means to an end as _everyone else_ here. Well, I would say that she has it even worse–seeing how thanks to the clones she can be killed and killed again, and all it would take is popping another out to replace her." Shinji shook his head. "It's just one more thing to hate the bastard for, and I encourage you to do it as much as you desire."

Misato still gave Ritsuko a look and got a shrug in return, before she nodded. "What next then, Commander?"

Shinji smiled some. "Well, we tell our staff what's going on."

* * *

The ride back towards Shinji's school was quiet. Neither Andrei nor Pavel had nothing to say to the boy and even if they did, they couldn't. The Commander's orders regarding the Third Child, as he was designated, were to simply watch over him and ensure his safety with as little interaction as possible. Both men of course wondered about the importance of the kid, aside from him being the Commander's son, and why he was given such a codename–but both were paid enough to justify not outright questioning it.

"So it's still called Gehirn, right?" Shinji asked.

Pavel looked back at Shinji, and then back at the road as Andrei drove.

"It's going to be reorganized into Nerv soon, the day after _she_ dies."

Pavel looked back again at Shinji. "What?"

"Korolev." Andrei's tone implied a warning.

Pavel dismissed it. "What do you mean, 'after she dies'?"

"She will die. The day after tomorrow in fact. Massive head and spinal trauma, twenty-two percent of brain matter found outside of the braincase, scratches on the forearms… but no previous evidence of suicidal thoughts or tendencies," Shinji droned, as if reading from an autopsy report.

The car pulled to the side of the road, and this time Andrei looked back with Pavel. Shinji smiled, he had their attention, now.

"Someone will die," Andrei reiterated. "You're talking like you can see the future."

"I can, that's my special power," Shinji revealed. "But no one knows about it except for you two."

Both men turned their attention forward again, dismissing his so-called "Special Power" outright. This kid, they decided, was just demented.

Shinji sat back in his seat and toyed with his SDAT player. "This person will die the day after tomorrow. Gehirn will become Nerv, and my Father will start working towards killing us all."

Both men appeared to pay him no mind, but Shinji was undaunted. "If this doesn't happen, go about your lives, but if it does, please come back to me and I'll tell you more about the future. Your very lives will depend on it."

Neither man reacted, and Shinji was dropped off at home without a word. Both men resolved to never speak of the incident, and wrote off the Commander's son as seriously disturbed thanks to having a bastard like Gendo Ikari for a father.

Three days later, as Shinji was walking to school yet again, the black sedan from Gehirn, now Nerv, hopped up onto the curb in front of him. A visibly shaken Andrei Rohmer and Pavel Korolev stepped out of the car, and stood before him.

"Naoko Akagi," Andrei said, "Killed herself by jumping from a railing in the Central Dogma."

"And you're now Nerv Department of Security Intelligence, yes?" Shinji asked.

Andrei and Pavel both nodded.

Shinji nodded slowly to the two men. "The end of the world is coming, gentlemen."

* * *

In the Central Dogma, Fuyutsuki lowered his head as he felt the disbelieving stares of Nerv's staff on him. At his side, Dr. Akagi looked down from the platform once occupied by the Professor and the Ex-Commander at Shinji, who stood with Misato amongst the betrayed staff trying to cope with what they had been brought aboard for.

"Seriously, this was all a lie?" Aoba asked. "You expected us to play along until you killed us all, old man?!"

"Not really much you could expect to do about it when it all came to a head, you know?" Shinji noted.

"In light of the recent change in command," Fuyutsuki responded to the growing clamor below, "The scenario that Gendo Ikari had initiated will be abandoned. As per Commander Shinji Ikari's wishes, the only role Nerv will play is the destruction of the Angels as per the original scenario outlined by the Human Instrumentality Project Committee. Gendo Ikari's ambitions will not be pursued."

Shinji nodded, while resisting the urge to smirk. "That's right," he said, "I came here to fight the Angels and preserve humanity, and that's what Nerv will do, no matter who or what will get in our way."

"Yes, but do we really need him in charge? He was in on it with Gendo," Hyuga pointed out.

"Fuyutsuki-sensei can be trusted, don't worry," Shinji reassured. "And if he can't we'll just kill him!"

"Dibs!" Aoba shouted before directing a dark look towards Fuyutsuki.

Shinji looked to Misato. "I like him; he and I are going to hang out."

"They're not a bad bunch at all, most of them at least…" Misato replied quietly. "Hyuga seems to want to get in my skirt."

"He'd probably look good in it, tell him where you shop."

This was going easier than Shinji thought, and he liked that. He'd expected a full-on walkout as a result of the coup and the revelations, but it looked like everyone was onboard with the new direction Nerv was going in. Some, like the cute blonde bridge bunny blowing him a kiss and holding up a card with her phone extension written down, seemed enthusiastic about it.

"Ooi, could you not?" Misato snapped at the woman.

"Ah, sorry ma'am!" the blonde quickly apologized, before mouthing "call me" to Shinji when Misato looked away.

A dark-haired, glasses wearing woman sitting next to the blonde smacked her upside her head, and smiled an apology to Shinji. Nodding back, he took a step back, and addressed the Bridge as a whole. "I'm glad that all of you are serious about the job you took here. That said, the next Angel will be here in exactly twelve days, I want NERV to be ready to receive our guest this time around."

"Yes sir, Commander Ikari!" Aoba declared.

"For God's sake… don't start fanboying over him like Maya does Dr. Akagi," Hyuga muttered.

"I do not fanboy over sempai!" Maya snapped.

"Yeah you do," both Hyuga and Aoba replied as Shinji turned and made for the exit. "Sub-Commander Fuyutsuki, I leave the bridge to you."

"Understood, Commander," Fuyutsuki replied.

Following Shinji out of the Central Dogma, Misato folded her arms as she weighed in on everything she learned in the past few hours. Gendo Ikari wanted to destroy the human race, The Committee wanted to destroy the human race, Shinji is ready to start a world war or three to save the human race, and now she and everyone else were onboard whether they wanted to be or not. Really, the idea of getting so fucking smashed that she wouldn't be able to remember the last thirty years of her life was suddenly an appealing one.

"Huh, I just realized I haven't made living arrangements, yet." Shinji's realization jogged her from her desire for alcohol poisoning.

Misato sighed. "Well, you're definitely not safe outside of Nerv."

"Of course I am! No one would be dumb enough to attempt anything." He wanted to believe so very badly.

"That's ridiculous. A man as smart as Gendo wouldn't just let his son walk in and take over. There could be people waiting to ambush you right now. They don't have to kill you to remove you."

"I can kill a man with a paperclip and a wet napkin, I'm not afraid of anything Father could throw at me." Shinji smiled. "Besides, I have the perfect insurance policy."

Misato frowned. "You wouldn't blow those nukes."

"I don't have to." As they walked down an otherwise empty and doorless corridor towards the escalators, Shinji asked, "Would it be okay if I lived with you, Misato?"

"What, with me? I barely have enough room for myself and a penguin." And her horrific alcoholism.

"You could live with me."

Misato was glad for once that she was tired as she was when Ritsuko came forward, literally out of nowhere, with her proposal, as she would've shot the woman had her reaction time been a half-second sharper. Whirling around and staring past her associate, the raven-haired Christmas Cake scoured the long, empty, sterile corridor for any door or passageway she could've come out of. Impossibly, she found none.

"You're going to tell me about those secret passages, Doctor," Shinji said lightly to her.

Misato relaxed and glowered directly at Ritsuko. "Me too, and no Shinji is not going to live with you."

"Why not, want him for yourself?" Ritsuko pouted at Misato, who flustered.

"Not in the slightest!" Misato roared. She wanted to go home, and get so drunk Pen-Pen would have a shot at her.

Shinji looked positively dejected. "Really?"

Misato **stared** at him. Shinji held his hands up and took a step back fearfully. Finding him subdued, she sighed. "I need a drink."

As the other woman fingered her temples, Ritsuko lightly made her way over to Shinji's side and hugged his arm. "Well, if you're going to go home and get smashed, I'll just take care of the Commander, deal?"

Misato's **stare** froze Ritsuko where she stood, and Shinji slowly scooted away from the doctor. "As much as I like Dr. Akagi's offer, I'd rather stay with you, Misato. I know well enough about how you live, and I'd be willing to clean up your apartment."

"Why with me?" Misato asked.

"The same reason I trusted to tell you everything," he replied.

Whatever future he saw must've painted her in a really strong light to him. It didn't make it any less creepy, though. "If you're willing to clean up after me, I hope you know what you're getting yourself into."

"I certainly do," Shinji said happily.

"I'll come with you then, you're both probably starving and Shinji doesn't need to be exposed to your cooking on his first night," Dr. Akagi said as she walked past them. "Your car's in the G Lot, right?"

Misato nodded and began to follow, Shinji in step with her. As she looked to him, she found that his expression was back to the calm that had first put her off about him, but it was much more refreshing to see, after seeing the wild emotional pitching he underwent. It didn't take nearly as long as it did for them to reach the parking lot as it did when Misato and Shinji first arrived. This was fine by Shinji, because after today, he was starving.

"So, what are we going to have for dinner?" He asked Dr. Akagi.

"Anything is better than Misato's cooking. I was thinking fried rice," Dr. Akagi replied.

"That's all you can make, anyway," Misato snapped.

"Which is one more thing than you can put together." Dr. Akagi met Misato's glare with a smile, which faded when she turned and looked ahead. Shinji and Misato stopped as well, when they found a half dozen Section 2 agents waiting between them and the latter's car.

Misato immediately didn't like this. "Section 2's finally moving?"

"Huh, they look new," Shinji quietly remarked.

"Third Child," one of the agents said as he stepped forward. "This is the end of the line-"

"Excuse me, are you new?" Shinji interrupted.

The agent paused.

"Because you look like you didn't get the memo," Shinji said. "I'm in charge."

"We only answer directly to The Commander," the agent replied.

Shinji nodded slowly. "Ah, then you are new."

Out of the shadows of the darkened the parking lot, more black suited, black sunglasses-wearing Section 2 agents emerged, surrounding the six agents, Shinji, Misato, and Dr. Akagi. Misato looked around at the other agents, tense. She didn't have enough bullets for all of them.

Dr. Akagi sighed. "Gendo is probably watching right now."

"Good," Shinji quipped.

"Come quietly, Third Child, and we will not harm you," the agent before them warned. "We will use any force necessary to subdue you if you resist, however."

Shinji raised a finger. "I have a counter offer." He put the finger to his head. "Put your weapons to your heads and kill yourselves, because you're surrounded."

The agents surrounding them drew their side arms, and pointed them at the six agents that confronted Shinji, numerous red dots from the lasers of their pistols dancing on their bodies.

Misato looked at the Section 2 agents that had materialized seemingly to come to Shinji's aid. "What's going on?"

"Remember when I said that a Section 2 agent supplied me my nuke?" Shinji asked. "Turns out, that there are a lot of people inside that particular organization who aren't too keen about being complicit in the end of the world."

Misato stared at Shinji with wide eyes, as the cavalry moved in to disarm the six agents and bring them to their knees with their hands behind their heads. "How long have they been in on this?"

Shinji bit his lower lip and hummed. "Since I was six?"

"How?" Misato asked.

"There are just some things I shouldn't know, Misato," Shinji said as one of the helpful Section 2 agents, an older foreigner, approached Shinji and handed him his sidearm. "Thank you, Korolev-san."

The older agent nodded curtly to his Commander. Walking over to the subdued agents, Shinji looked down at their leader. "You must be pretty well paid to be willing to do this kind of thing."

The defeated agent looked up at the older man. "Korolev, you bastard. How long have you been with him-?!"

Shinji smacked him across the face with his pistol. "You're on the wrong side, working for Father. But I'm a forgiving person, so you have two choices: Join me or I hurt you."

"We swore to protect Nerv and Proje-mph." Shinji had stuck the barrel of the pistol in the man's mouth.

"No rhetoric. Nod if you're with me, shake your head if you're against me," Shinji said, moving his head to emphasize.

Defiant, the agent shook his head.

Shinji smiled back, and turned the pistol so that the muzzle was pointed at his lower right jaw. A messy pop sounded, as he squeezed the trigger and blew out part of the man's mouth.

"Jesus Christ," Misato gasped, as the agent fell over, letting out a gurgling scream of pain. Dr. Akagi just watched, silent.

Wiping off the barrel of the gun with his shirt, Shinji flipped it over and handed it back grip-first to Pavel. "Again, thank you Korolev-san."

The Russian nodded and took the gun. "What shall we do with them?"

"Whatever you like, I'm done for the night." Shinji looked to Misato and Dr. Akagi. "Sorry about that."

Misato looked at the screaming man, and then back to Shinji. "It's okay, they're our enemy."

Shinji refrained from smiling for once, though he really wanted to.

Dr. Akagi was in awe. "The nuke was never what got you in, it was just to take over without an actual fight. You've had Nerv in your hands all this time."

Shinji looked over to her. "You're right, I did. Feel free to worship the ground I walk on, Ritsuko Akagi."

Honestly, she wanted to worship him right here and now in front of all of Section 2. But that would've been awkward.

* * *

Sitting on the hood of Andrei and Pavel's car, Shinji ate a popsicle as he watched the sun set. In front of him, Andrei and Pavel weighed heavily on what they had learned about the future. Looking up from his feet, Andrei turned and looked at the boy.

"This is what will happen, regardless of any outcome."

"If I don't act, yes, this is what will happen," the child replied.

Andrei looked down again, and after a long silence, asked. "How do we stop it?"

Shinji bit off the end of the popsicle, and swallowed it down. "It will have to be more than just us. We will need many people, to take over Nerv."

Pavel hummed. "Then, you will need Section 2."

Shinji's brows rose. "Eh?"

Pavel looked from his feet, and directly at Shinji. "We're well connected inside the Agency. Give us time, and it will be yours."

Shinji nodded. "Okay, Korolev-san, Rohmer-san. I leave that to you."

"You will need more than just Section 2, if you want to fight The Committee, though," Rohmer pointed out.

Shinji nodded again. "I'd need a lot more people, a whole world of people. Can you help me with that, Rohmer-san?"

At that, Andrei stared off into the distance, before he replied…

"I know some people, yes."

A wide, frightening smile spread across Shinji's lips.

* * *

A/N: Shinji Ikari controls the horizontal, controls the vertical.


End file.
